Edits/corrections to doc pages 2315-2589

doc/src/pair_cosine_squared.rst

@@ -14,12 +14,12 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   pair_coeff i j eps sigma
-   pair_coeff i j eps sigma cutoff
-   pair_coeff i j eps sigma wca
-   pair_coeff i j eps sigma cutoff wca
+   pair_coeff I J eps sigma
+   pair_coeff I J eps sigma cutoff
+   pair_coeff I J eps sigma wca
+   pair_coeff I J eps sigma cutoff wca
 
-* i,j = a particle type
+* I, J = a particle type
 * eps = interaction strength, i.e. the depth of the potential minimum (energy units)
 * sigma = distance of the potential minimum from 0
 * cutoff = the cutoff distance for this pair type, if different from global (distance units)

doc/src/pair_coul_diel.rst

@@ -28,7 +28,7 @@ Description
 
 Style *coul/diel* computes a Coulomb correction for implicit solvent
 ion interactions in which the dielectric permittivity is distance dependent.
-The dielectric permittivity epsilon_D(r) connects to limiting regimes:
+The dielectric permittivity :math:`\epsilon_D(r)` connects to limiting regimes:
 One limit is defined by a small dielectric permittivity (close to vacuum)
 at or close to contact separation between the ions. At larger separations
 the dielectric permittivity reaches a bulk value used in the regular Coulomb
@@ -45,7 +45,7 @@ where :math:`r_{me}` is the inflection point of :math:`\epsilon_D(r)` and :math:
 defining length scale. C is the same Coulomb conversion factor as in the
 pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb
 interaction between ions is corrected at small distances r. The lower
-limit of epsilon_D(r->0)=5.2 due to dielectric saturation :ref:`(Stiles) <Stiles>`
+limit of :math:`\epsilon_D(r \to 0) = 5.2` due to dielectric saturation :ref:`(Stiles) <Stiles>`
 while the Coulomb interaction reaches its bulk limit by setting
 :math:`\epsilon_D(r \to \infty) = \epsilon`, the bulk value of the solvent which is 78
 for water at 298K.

doc/src/pair_coul_slater.rst

@@ -43,7 +43,7 @@ Examples
 Description
 """""""""""
 
-Styles *coul/slater* compute electrostatic interactions in mesoscopic models
+Styles *coul/slater/** compute electrostatic interactions in mesoscopic models
 which employ potentials without explicit excluded-volume interactions.
 The goal is to prevent artificial ionic pair formation by including a charge
 distribution in the Coulomb potential, following the formulation of

doc/src/pair_dipole.rst

@@ -129,7 +129,7 @@ torques do not act symmetrically.  These formulas are discussed in
 Also note, that in the code, all of these terms (except Elj) have a
 :math:`C/\epsilon` prefactor, the same as the Coulombic term in the
 LJ + Coulombic pair styles discussed :doc:`here <pair_lj>`.  C is an
-energy-conversion constant and epsilon is the dielectric constant
+energy-conversion constant and :math:`\epsilon` is the dielectric constant
 which can be set by the :doc:`dielectric <dielectric>` command.  The
 same is true of the equations that follow for other dipole pair
 styles.

doc/src/pair_dpd.rst

@@ -118,7 +118,7 @@ atoms types via the :doc:`pair_coeff <pair_coeff>` command are:
 
 The cutoff coefficient is optional.
 
-The GPU-accelerated versions of these styles are implemented based on
+Styles with a *gpu* suffix are implemented based on
 the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
 
 .. note::

doc/src/pair_eff.rst

@@ -122,14 +122,6 @@ distance.  The recommended cutoff for this pair style should follow
 the minimum image criterion, i.e. half of the minimum unit cell
 length.
 
-Style *eff/long* (not yet available) computes the same interactions as
-style *eff/cut* except that an additional damping factor is applied so
-it can be used in conjunction with the
-:doc:`kspace_style <kspace_style>` command and its *ewald* or *pppm*
-option.  The Coulombic cutoff specified for this style means that
-pairwise interactions within this distance are computed directly;
-interactions outside that distance are computed in reciprocal space.
-
 This potential is designed to be used with :doc:`atom_style electron <atom_style>` definitions, in order to handle the
 description of systems with interacting nuclei and explicit electrons.
 
@@ -145,11 +137,6 @@ For *eff/cut*, the cutoff coefficient is optional.  If it is not used
 (as in some of the examples above), the default global value specified
 in the pair_style command is used.
 
-For *eff/long* (not yet available) no cutoff will be specified for an
-individual I,J type pair via the :doc:`pair_coeff <pair_coeff>` command.
-All type pairs use the same global cutoff specified in the pair_style
-command.
-
 ----------
 
 The *limit/eradius* and *pressure/evirials* keywords are optional.
@@ -190,7 +177,7 @@ representations, after the "ecp" keyword.
 
 .. note::
 
-   there are two different pressures that can be reported for eFF
+   There are two different pressures that can be reported for eFF
    when defining this pair_style, one (default) that considers electrons
    do not contribute radial virial components (i.e. electrons treated as
    incompressible 'rigid' spheres) and one that does.  The radial

doc/src/pair_extep.rst

@@ -33,7 +33,7 @@ none
 Related commands
 """"""""""""""""
 
-`pair_tersoff <pair tersoff>`
+:doc:`pair_tersoff <pair_tersoff>`
 
 Default
 """""""

doc/src/pair_gran.rst

@@ -80,7 +80,7 @@ The two Hookean styles use this formula:
 
    F_{hk} = (k_n \delta \mathbf{n}_{ij} -
    m_{eff} \gamma_n\mathbf{ v}_n) -
-   (k_t \mathbf{ \Delta s}_t +
+   (k_t \boldsymbol{\Delta} \mathbf{s}_t +
    m_{eff} \gamma_t \mathbf{v}_t)
 
 The Hertzian style uses this formula:
@@ -91,7 +91,7 @@ The Hertzian style uses this formula:
      \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}}
      \Big[ (k_n \delta \mathbf{n}_{ij} -
        m_{eff} \: \gamma_n \mathbf{ v}_n) -
-       (k_t \mathbf{ \Delta s}_t +
+       (k_t \boldsymbol{\Delta} \mathbf{s}_t +
        m_{eff} \: \gamma_t \mathbf{v}_t) \Big]
 
 In both equations the first parenthesized term is the normal force
@@ -114,7 +114,7 @@ The other quantities in the equations are as follows:
 * :math:`\gamma_n` = viscoelastic damping constant for normal contact
 * :math:`\gamma_t` = viscoelastic damping constant for tangential contact
 * :math:`m_{eff} = M_i M_j / (M_i + M_j) =` effective mass of 2 particles of mass M_i and M_j
-* :math:`\mathbf{\Delta s}_t =` tangential displacement vector between 2 particles       which is truncated to satisfy a frictional yield criterion
+* :math:`\boldsymbol{\Delta} \mathbf{s}_t =` tangential displacement vector between 2 particles which is truncated to satisfy a frictional yield criterion
 * :math:`n_{ij} =` unit vector along the line connecting the centers of the 2 particles
 * :math:`V_n =` normal component of the relative velocity of the 2 particles
 * :math:`V_t =` tangential component of the relative velocity of the 2 particles

doc/src/pair_granular.rst

@@ -328,7 +328,7 @@ keyword also affects the tangential damping.  The parameter
 literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`,
 :ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`).  The relative
 tangential velocity at the point of contact is given by
-:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\mathbf{\Omega}_i + R_j\mathbf{\Omega}_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}\ \mathbf{n}`,
+:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\boldsymbol{\Omega}_i + R_j\boldsymbol{\Omega}_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}\ \mathbf{n}`,
 :math:`\mathbf{v}_r = \mathbf{v}_j - \mathbf{v}_i` .
 The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\mathbf{v_{t,rel}}\|` .
 
@@ -548,7 +548,7 @@ the tangential force:
 
    \mathbf{F}_{roll,0} =  k_{roll} \mathbf{\xi}_{roll}  - \gamma_{roll} \mathbf{v}_{roll}
 
-Here, :math:`\mathbf{v}_{roll} = -R(\mathbf{\Omega}_i - \mathbf{\Omega}_j) \times \mathbf{n}` is the relative rolling
+Here, :math:`\mathbf{v}_{roll} = -R(\boldsymbol{\Omega}_i - \boldsymbol{\Omega}_j) \times \mathbf{n}` is the relative rolling
 velocity, as given in :ref:`Wang et al <Wang2015>` and
 :ref:`Luding <Luding2008>`. This differs from the expressions given by :ref:`Kuhn and Bagi <Kuhn2004>` and used in :ref:`Marshall <Marshall2009>`; see :ref:`Wang et al <Wang2015>` for details. The rolling displacement is given by:
 

doc/src/pair_lj_cut_coul.rst

@@ -188,7 +188,7 @@ specified for this style means that pairwise interactions within this
 distance are computed directly; interactions outside that distance are
 computed in reciprocal space.
 
-Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf
+Style *lj/cut/coul/wolf* adds a Coulombic pairwise interaction via the Wolf
 summation method, described in :ref:`Wolf <Wolf3>`, given by:
 
 .. math::